Variant report

Variant	rs2852512
Chromosome Location	chr6:101846554-101846555
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr6:101846554-101847310	H1-hESC	embryonic stem cell:	n/a	n/a
2	GATA2	chr6:101846458-101848664	SH-SY5Y	brain:	n/a	chr6:101848310-101848321 chr6:101848308-101848317 chr6:101848310-101848317 chr6:101848308-101848317 chr6:101848307-101848319 chr6:101848308-101848318 chr6:101848310-101848317 chr6:101848305-101848321 chr6:101848310-101848317
3	CEBPB	chr6:101846465-101847049	IMR90	lung:	n/a	n/a
4	CEBPB	chr6:101846497-101846870	H1-hESC	embryonic stem cell:	n/a	n/a
5	REST	chr6:101846284-101847726	H1-neurons	neurons:	n/a	chr6:101846883-101846896 chr6:101847549-101847562
6	POLR2A	chr6:101846500-101847074	H1-neurons	neurons:	n/a	n/a
7	MXI1	chr6:101845906-101852010	SK-N-SH	brain:	n/a	chr6:101849846-101849861 chr6:101849844-101849859
8	RAD21	chr6:101846514-101847108	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
GRIK2	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1160258	0.83[ASN][1000 genomes]
rs1415946	0.87[ASW][hapmap];0.81[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.80[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs17658674	0.83[ASN][1000 genomes]
rs1948050	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2518173	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2518319	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2579929	0.97[EUR][1000 genomes]
rs2629982	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2787573	0.97[EUR][1000 genomes]
rs283186	0.86[ASN][1000 genomes]
rs2852497	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2852500	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852501	0.91[AFR][1000 genomes]
rs2852502	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852504	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852505	0.97[EUR][1000 genomes]
rs2852506	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852508	0.87[ASW][hapmap];0.81[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.80[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2852509	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852510	0.97[EUR][1000 genomes]
rs2852511	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852513	0.97[EUR][1000 genomes]
rs2852514	0.97[EUR][1000 genomes]
rs471631	1.00[ASN][1000 genomes]
rs473846	1.00[ASN][1000 genomes]
rs480221	1.00[ASN][1000 genomes]
rs484819	1.00[ASN][1000 genomes]
rs489458	1.00[ASN][1000 genomes]
rs493123	1.00[ASN][1000 genomes]
rs496596	0.84[EUR][1000 genomes]
rs500305	1.00[ASN][1000 genomes]
rs503387	0.90[EUR][1000 genomes]
rs504406	1.00[ASN][1000 genomes]
rs504408	1.00[ASN][1000 genomes]
rs528879	1.00[ASN][1000 genomes]
rs542820	1.00[ASN][1000 genomes]
rs542923	1.00[ASN][1000 genomes]
rs546327	1.00[ASN][1000 genomes]
rs566507	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570556	0.84[EUR][1000 genomes]
rs577503	1.00[ASN][1000 genomes]
rs579069	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs584655	1.00[ASN][1000 genomes]
rs594870	1.00[ASN][1000 genomes]
rs600842	1.00[ASN][1000 genomes]
rs608847	1.00[ASN][1000 genomes]
rs632956	0.95[EUR][1000 genomes]
rs636796	1.00[ASN][1000 genomes]
rs638255	1.00[ASN][1000 genomes]
rs661064	0.90[EUR][1000 genomes]
rs662360	0.89[EUR][1000 genomes]
rs662916	1.00[ASN][1000 genomes]
rs668267	1.00[ASN][1000 genomes]
rs675259	0.92[EUR][1000 genomes]
rs683149	1.00[ASN][1000 genomes]
rs684160	1.00[ASN][1000 genomes]
rs685002	1.00[ASN][1000 genomes]
rs687497	0.89[EUR][1000 genomes]
rs697440	1.00[ASN][1000 genomes]
rs697441	1.00[ASN][1000 genomes]
rs808952	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020400	chr6:101172705-101981665	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv538390	chr6:101172705-101981665	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2852512	TOX3	trans	lymphoblastoid	seeQTL
rs2852512	SNX7	trans	lymphoblastoid	seeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101842200-101846600	Weak transcription	Pancreas	Pancrea
2	chr6:101842200-101849600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:101842400-101849600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:101842800-101846800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:101843200-101846600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:101843200-101846800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:101846000-101846800	Active TSS	Brain Angular Gyrus	brain
8	chr6:101846000-101849600	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr6:101846200-101846600	Active TSS	Fetal Brain Female	brain
10	chr6:101846200-101847200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:101846400-101846600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
12	chr6:101846400-101846600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:101846400-101846600	Bivalent Enhancer	NH-A	brain
14	chr6:101846400-101846800	Bivalent Enhancer	Fetal Kidney	kidney
15	chr6:101846400-101847000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
16	chr6:101846400-101847800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr6:101846400-101847800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr6:101846400-101847800	Active TSS	Right Atrium	heart
19	chr6:101846400-101848000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
20	chr6:101846400-101848000	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr6:101846400-101848200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
22	chr6:101846400-101849200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
23	chr6:101846400-101851600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links